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Urinary Bladder

The urinary bladder is a hollow, muscular organ that stores and releases urine from the body.
It plays a crucial role in the urinary system, serving as a temporary reservoir for urine before it is eliminated.
The bladder's walls are composed of smooth muscle tissue, allowing it to expand and contract to accommodate changes in urine volume.
Proper bladder function is essential for maintaining urinary continence and overall urinary tract health.
Exploring the power of AI-driven platforms like PubCompare.ai can help researchers optimize urinary bladder research, identify the most relevant protocols, and enhance reproducibility and accuracy in their studies.
Discover the latest advancements in this important area of medical research.

Most cited protocols related to «Urinary Bladder»

SignatureAnalyzer uses a Bayesian variant of NMF that infers the number of signatures through the automatic relevance determination technique and delivers highly interpretable and sparse representations for both signature profiles and attributions that strike a balance between data fitting and model complexity. Further details of the actual implementation of the computational approach have previously been published9 (link),27 (link),64 (link). SignatureAnalyzer was applied by using a two-step signature extraction strategy using 1,536 pentanucleotide contexts for SBSs, 83 indel features and 78 DBS features. In addition to the separate extraction of SBS, indel and DBS signatures, we performed a ‘COMPOSITE’ signature extraction based on all 1,697 features (1,536 SBS + 78 DBS + 83 indel). For SBSs, the 1,536 SBS COMPOSITE signatures are preferred; for DBSs and indels, the separately extracted signatures are preferred.
In step 1 of the two-step extraction process, global signature extraction was performed for the samples with a low mutation burden (n = 2,624). These excluded hypermutated tumours: those with putative polymerase epsilon (POLE) defects or mismatch repair defects (microsatellite instable tumours), skin tumours (which had intense UV-light mutagenesis) and one tumour with temozolomide (TMZ) exposure. Because the underlying algorithm of SignatureAnalyzer performs a stochastic search, different runs can produce different results. In step 1, we ran SignatureAnalyzer 10 times and selected the solution with the highest posterior probability. In step 2, additional signatures unique to hypermutated samples were extracted (again selecting the highest posterior probability over ten runs) while allowing all signatures found in the samples with low mutation burden, to explain some of the spectra of hypermutated samples. This approach was designed to minimize a well-known ‘signature bleeding’ effect or a bias of hyper- or ultramutated samples on the signature extraction. In addition, this approach provided information about which signatures are unique to the hypermutated samples, which was later used when attributing signatures to samples.
A similar strategy was used for signature attribution: we performed a separate attribution process for low- and hypermutated samples in all COMPOSITE, SBS, DBS and indel signatures. For downstream analyses, we preferred to use the COMPOSITE attributions for SBSs and the separately calculated attributions for DBSs and indels. Signature attribution in samples with a low mutation burden was performed separately in each tumour type (for example, Biliary–AdenoCA, Bladder–TCC, Bone–Osteosarc, and so on). Attribution was also performed separately in the combined microsatellite instable tumours (n = 39), POLE (n = 9), skin melanoma (n = 107) and TMZ-exposed samples (syn11738314). In both groups, signature availability (which signatures were active, or not) was primarily inferred through the automatic relevance determination process applied to the activity matrix H only, while fixing the signature matrix W. The attribution in samples with a low mutation burden was performed using only signatures found in the step 1 of the signature extraction. Two additional rules were applied in SBS signature attribution to enforce biological plausibility and minimize a signature bleeding: (i) allow SBS4 (smoking signature) only in lung, head and neck cases; and (ii) allow SBS11 (TMZ signature) in a single GBM sample. This was enforced by introducing a binary, signature-by-sample signature indicator matrix Z (1, allowed; 0, not allowed), which was multiplied by the H matrix in every multiplication update of H. No additional rules were applied to indel or DBS signature attributions, except that signatures found in hypermutated samples were not allowed in samples with a low mutation burden.
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Publication 2020
Bile Biopharmaceuticals Bones Familial Atypical Mole-Malignant Melanoma Syndrome Head INDEL Mutation Lung Microsatellite Instability Mismatch Repair Mutagenesis Mutation Neck Neoplasms Skin Neoplasms Temozolomide Ultraviolet Rays Urinary Bladder
Results are based in part upon data generated by TCGA Research Network (http://cancergenome.nih.gov/). We aggregated TCGA transcriptomic and RPPA data from public repositories, listed in the “Data availability” section. RNA-seq expression data were processed by TCGA at the gene level, rather than at the transcript level. Tumors spanned 32 different TCGA projects, each project representing a specific cancer type, listed as follows: LAML, acute myeloid leukemia; ACC, adrenocortical carcinoma; BLCA, bladder urothelial carcinoma; LGG, lower grade glioma; BRCA, breast invasive carcinoma; CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma; CHOL, cholangiocarcinoma; CRC, colorectal adenocarcinoma (combining COAD and READ projects); ESCA, esophageal carcinoma; GBM, glioblastoma multiforme; HNSC, head and neck squamous cell carcinoma; KICH, kidney chromophobe; KIRC, kidney renal clear cell carcinoma; KIRP, kidney renal papillary cell carcinoma; LIHC, liver hepatocellular carcinoma; LUAD, lung adenocarcinoma; LUSC, lung squamous cell carcinoma; DLBC, lymphoid neoplasm diffuse large B-cell lymphoma; MESO, mesothelioma; OV, ovarian serous cystadenocarcinoma; PAAD, pancreatic adenocarcinoma; PCPG, pheochromocytoma and paraganglioma; PRAD, prostate adenocarcinoma; SARC, sarcoma; SKCM, skin cutaneous melanoma; STAD, stomach adenocarcinoma; TGCT, testicular germ cell tumors; THYM, thymoma; THCA, thyroid carcinoma; UCS, uterine carcinosarcoma; UCEC, uterine corpus endometrial carcinoma; UVM, uveal melanoma. Cancer molecular profiling data were generated through informed consent as part of previously published studies and analyzed per each original study’s data use guidelines and restrictions.
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Publication 2019
4-carboxyphenylglyoxal Adenocarcinoma Adenocarcinoma of Lung Adrenocortical Carcinoma Breast Carcinoma Carcinoma, Thyroid Carcinoma, Transitional Cell Carcinosarcoma Cells Cholangiocarcinoma Chromophobia Chronic Obstructive Airway Disease Diffuse Large B-Cell Lymphoma Endocervix Endometrial Carcinoma Esophageal Cancer Familial Atypical Mole-Malignant Melanoma Syndrome Gene Expression Profiling Genes Glioblastoma Multiforme Glioma Hepatocellular Carcinomas Hypernephroid Carcinomas Kidney Leukemia, Myelocytic, Acute Lung Lymph Malignant Neoplasms Mesothelioma Neck Neoplasms Ovary Pancreas Paraganglioma Pheochromocytoma Prostate Renal Cell Carcinoma RNA-Seq Sarcoma Serous Cystadenocarcinoma Squamous Cell Carcinoma Squamous Cell Carcinoma of the Head and Neck Stomach Testicular Germ Cell Tumor Thymoma Urinary Bladder Uterus Uveal melanoma X-Ray Photoelectron Spectroscopy
Tumour and normal samples were obtained with institutional review board-approved consent and processed using a modified AllPrep kit (Qiagen) to obtain purified DNA and RNA. Quality-control analyses revealed only modest batch effects (Supplementary Text S13.1). The tumours were profiled using Affymetrix SNP 6.0 microarrays for SCNAs, low-pass WGS (HiSeq) for SCNAs and translocations, RNA-seq (HiSeq) for mRNA and miRNA expression, Illumina Infinium (HumanMethylation450) arrays for DNA methylation, HiSeq for exome sequencing and RPPA for protein expression and phosphorylation. Statistical analysis and biological interpretation of the data were spearheaded by the TCGA Genome Data Analysis Centers. Sequence files are in CGHub (https://cghub.ucsc.edu/). All other molecular, clinical and pathological data are available through the TCGA Data Portal (https://tcga-data.nci.nih.gov/tcga/). Data matrices, molecular analysis results and supporting information are at http://tcga-data.nci.nih.gov/docs/publications/bladder_2013/. The data can be explored through a compendium of Next-Generation Clustered Heat Maps (http://bioinformatics.mdanderson.org/main/TCGA/Supplements/NGCHM-BLCA), the cBio Cancer Genomics Portal (http://cbioportal.org), PARADIGM (http://sysbio.soe.ucsc.edu/paradigm/tutorial/), SpliceSeq (http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview), MBatch batch effects assessor (http://bioinformatics.mdanderson.org/tcgabatcheffects) and Regulome Explorer (http://explorer.cancerregulome.org/). Also see Supplementary Materials.
Publication 2014
Biopharmaceuticals Dietary Supplements DNA Chips Ethics Committees, Research Genome Malignant Neoplasms Methylation Microarray Analysis MicroRNAs Microtubule-Associated Proteins Neoplasms Phosphorylation RNA, Messenger RNA-Seq Translocation, Chromosomal type III polyketide synthase Urinary Bladder

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Publication 2009
Chronic Pain Coitus Diagnosis Ejaculation Males Pain Penis Perineum Prostatitis System, Genitourinary Testis Urethra Urinary Bladder Urine Vagina Woman

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Publication 2014
Biopsy BLOOD Blood Cells Bones Brain Cells Circulating Neoplastic Cells Collagenase Erythrocytes Ficoll Growth Factor Heparin Homo sapiens Leukocytes Liver Malignant Neoplasms matrigel Neoplasm Metastasis Nodes, Lymph Organoids Patients Pleural Effusion Prostate Prostate Cancer Stem Cells Tissues Type II Mucolipidosis Urinary Bladder

Most recents protocols related to «Urinary Bladder»

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Example 4

Initial in vivo studies focused on soft tissue models of MSSA infection. This included a mouse thigh infection model and rat triceps model. FIG. 2 shows data for the accumulation of [18F]F-PABA in the triceps of an infected rat. Fifty μL of 109 CFU of Newman S. aureus BHI culture was injected into the right triceps of a rat. After 10-15 hr the rats were imaged following iv administration of 0.8-1.2 mCi of [18F]F-PABA. The images clearly show the accumulation of radioactivity in the right but not the left triceps. In addition to monitoring the time course of [18F]F-PABA biodistribution, we also quantified tracer levels by postmortem ex vivo counting. While the [18F]F-PABA distributed to all tissues and organs with the exception of the brain, significant tracer accumulation was only observed in the right triceps, as well as the kidney, bladder and GI tracts due to tracer clearance. At 60 min tracer levels were 5.4× higher in the infected right triceps compared to the uninfected left triceps. This compares favorably with other tracers.

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Patent 2024
4-Aminobenzoic Acid Autopsy Brain Gastrointestinal Tract Infection Kidney Mus Radioactivity Rattus Thigh Tissues Urinary Bladder

Example 16

The antitumor activity of exemplary MEK inhibitor compounds is evaluated in vivo using human cell line derived xenografts (CDX) grown in immunodeficient mice. For these studies, AsPC1 (pancreatic cell line with KRAS G12D mutation), NCI-H2122 (lung cell line with KRAS G12C mutation), and 5637 (bladder cell line with CRAF amplification) models are used. In addition, HCT-116 (colorectal cell line with KRAS G13D mutation), SKM-1 (AML cell line with KRAS K117N mutation), and OCI-AML-3 (AML cell line with NRAS Q61L mutation) models are used. The tumor cell lines (AsPC-1, NCI-H2122, 5637, and HCT-116 cells) are maintained in vitro as monolayer culture in medium at 37° C. in an atmosphere of 5% CO2 in air. The tumor cell lines (SKM-1 and OCI-AML-3 cells) are maintained in vitro as a suspension in medium at 37° C. in an atmosphere of 5% CO2 in air. The tumor cells are routinely sub-cultured before confluence by trypsin-EDTA treatment, not to exceed 4-5 passages. The cells growing in an exponential growth phase are harvested for tumor inoculation. AsPC1, NCI-H2122, and OCI-AML-3 tumors are implanted into Balb/c nude mice. HCT-116 tumors are implanted into Nu/Nu mice. 5637 and SKM-1 tumors are implanted into NOG mice. Each mouse is inoculated subcutaneously on the right flank with tumor cells in a 1:1 mixture with matrigel. Tumors are allowed to grow to approximately 150-200 mm3. At this time, mice are assigned to groups such that the mean tumor volume is the same for each treatment group. The MEK inhibitor compound treatments are administrated to the tumor-bearing mice via oral gavage. Throughout the study, mouse body weight and tumor volume are recorded. The measurement of tumor size is conducted twice weekly with a caliper and recorded. The tumor volume (mm3) is estimated using the formula: TV=a×b2/2, where “a” and “b” are long and short diameters of a tumor, respectively.

In the AsPC-1 model, exemplary MEK inhibitor I-2 was treated at 3 mg/kg QD and a percent TGI (tumor growth inhibition) on Day 21 of 83.4% was observed. The average body weight gain observed on Day 21 was 2.4%.

In the NCI-H2122 model, exemplary MEK inhibitor 1-2 was treated at 3 mg/kg QD and a percent TGI on Day 31 of 104% was observed. The average body weight loss observed on Day 31 was 1.5%.

In the 5637 model, exemplary MEK inhibitor I-2 was treated at 3 mg/kg QD and a percent TGI on Day 21 of 111% was observed. The average body weight loss observed on Day 21 was 6.8%.

In the HCT-116 model, exemplary MEK inhibitor I-2 was treated at 2 mg/kg QD, 3 mg/kg QOD or 6 mg/kg QOD and a percent TGIs on Day 20 of 102.9%, 98.1%, and 98%, respectively, were observed. The average body weight gain observed on Day 20 was 4%, 5.5%, and 12.1%, respectively.

In the SKM-1 model, exemplary MEK inhibitor I-2 was treated at 1 mg/kg QD, 3 mg/kg QD or 6 mg/kg QOD and venetoclax was treated at 100 mg/kg QD and a percent TGIs on Day 22 of 97.7%, 98.4%, 96.2%, and 46.6% respectively, were observed. The average body weight loss observed on Day 22 for the 3 mg/kg QD group was 1.2%, whereas weight gain was observed in 1 mg/kg QD, 6 mg/kg QOD and venetoclax groups (1.2%, 3.9, and 7.5%, respectively).

In the OCI-AML-3 model, exemplary MEK inhibitor I-2 was treated at 1 mg/kg QD, 3 mg/kg QD or 6 mg/kg QOD, and venetoclax was treated at 100 mg/kg QD and a percent TGIs on Day 15 of 94.8, 98.6, 95.2, and 13% respectively, were observed. The average body weight loss observed on Day 15 for the 1 and 3 mg/kg QD group was 2.9% and 7.8%, respectively, whereas weight gain was observed in 6 mg/kg QOD and venetoclax groups (3.3% and 8.3%, respectively).

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Patent 2024
Atmosphere Body Weight Cancer Vaccines Cell Line, Tumor Cell Lines Cells Edetic Acid HCT116 Cells Heterografts Homo sapiens Human Body Immunologic Deficiency Syndromes K-ras Genes Lung MAP2K2 protein, human matrigel MEK inhibitor I Mice, Inbred BALB C Mice, Nude Mus Mutation Neoplasms NRAS protein, human Pancreas Psychological Inhibition Raf1 protein, human Trypsin Tube Feeding Urinary Bladder venetoclax
To determine the sample size for our study, we performed a power analysis for logistic regression using WebPower (https://webpower.psychstat.org/). The association of intensity score, staining distribution score, and final immunohistochemical score with sample groups (UC, cystitis, normal canine urinary bladder) for VEGFR2, KIT, PDGFR-β, and CDK4 was determined. Fisher exact tests were performed to evaluate for independence and for pairwise comparison (i.e., UC vs. cystitis, UC vs. normal, cystitis vs. normal). Risk factors for UC development were evaluated using conditional logistic regression analyses. Cox proportional hazard regression analysis was used to evaluate the correlation between the parameters under investigation and the clinical outcome. Dogs that were lost to follow-up were censored in the Cox proportional hazard regression analysis. Differences were considered significant at p ≤ 0.05. All statistical analyses were performed via computer software (R 4.0.2, https://www.r-project.org/). Logistic regression was used to identify risk factors for UC using a generalized linear model through the “glm” function in R. Binomial regression was used to evaluate the development of UC and cystitis relative to normal samples.
Publication 2023
Canis familiaris Cystitis Platelet-Derived Growth Factor beta Receptor Urinary Bladder Vascular Endothelial Growth Factor Receptor-2
We selected formalin-fixed, paraffin-embedded samples of UC, cystitis, and normal canine bladders from the archive at the Veterinary Pathology Diagnostic Services at the University of Sydney (New South Wales, Australia). An anatomic pathologist confirmed the diagnoses of UC, cystitis, and normal before immunohistochemical analysis was performed. Carcinoma cases had also been confirmed by histopathology for tumor origin in the kidney, bladder, or urethra. Samples without propria-submucosa were excluded. Information collected from the medical records included age, sex, breed, date of treatment initiation, treatment protocol, outcome, and, when available, cause of death. Cause of death was classified as: related to primary UC (such as acute renal failure, urinary obstruction, uremia), related to metastatic UC, or associated with other diseases unrelated to UC. All cases were assessed histologically and graded according to the World Health Organization (WHO) tumor classification system 201610 (link)
; tumors are differentiated into 3 grades: G1, G2, and G3. The lowest grade (G1) displays slim papilla with no atypia; the highest grade (G3) displays major atypia with marked loss of normal architecture. A classification of G2 covers the wide spectrum of lesions seen between G1 and G3 and includes increasing layers within the papilla and rare atypia.
Publication 2023
Canis familiaris Carcinoma Cystitis Diagnosis Formalin Kidney Failure, Acute Kidney Neoplasm Neoplasms Nipples Paraffin Embedding Pathologists Treatment Protocols Uremia Urethra Urinary Bladder Urine Vision
Staining was compared among UC, inflammatory non-neoplastic (cystitis), and normal urinary bladder samples. A histologically confirmed canine metastatic hemangiosarcoma served as a positive control for VEGFR2; a canine liposarcoma served as a positive control for KIT; a canine squamous cell carcinoma served as a positive control for PDGFR-β; and a canine mesenchymal neoplasm was used as a positive control for CDK4 (Suppl. Figs. 1–4). A negative control that omitted incubation with the primary antibody (antibody diluent with no antibody) was included for each sample.
Samples were evaluated for urothelial expression of VEGFR2, KIT, PDGFR-β, and CDK4 in an anonymized study by 3 veterinary pathologists, each from a different institution. A qualitative immunohistochemical assessment was performed to evaluate staining intensity. As described previously,32
staining intensity was assessed over the whole sample at 200 × magnification (0 = none, 1 = mild, 2 = moderate, 3 = intense). Staining distribution (% urothelial cells affected) was evaluated semi-quantitatively over 10 hpfs at 400 × magnification (0 = no staining, 1 = >0% to <10% positive, 2 = ≥10% to <25% positive, 3 = ≥25% to 50% positive, 4 = ≥50% to <75% positive, 5 = ≥75% positive). To calculate a score for every sample, the average scores were taken and called the standardized score. After averaging the 10 selected fields, a final immunohistochemical score for each sample was calculated by multiplying the intensity (qualitative) standardized score by the staining distribution (semi-quantitative) standardized score, as described previously.3 (link),22 (link)
Publication 2023
Canis familiaris Cells Cystitis Figs Hemangiosarcoma Immunoglobulins Inflammation Liposarcoma Mesenchyma Neoplasms Pathologists Platelet-Derived Growth Factor beta Receptor Squamous Cell Carcinoma Urinary Bladder Urothelium Vascular Endothelial Growth Factor Receptor-2

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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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RPMI 1640 medium is a commonly used cell culture medium developed at Roswell Park Memorial Institute. It is a balanced salt solution that provides essential nutrients, vitamins, and amino acids to support the growth and maintenance of a variety of cell types in vitro.
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DMEM (Dulbecco's Modified Eagle's Medium) is a cell culture medium formulated to support the growth and maintenance of a variety of cell types, including mammalian cells. It provides essential nutrients, amino acids, vitamins, and other components necessary for cell proliferation and survival in an in vitro environment.
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
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The SV-HUC-1 is a type of laboratory equipment designed for the culturing and maintenance of human urinary bladder cells. It provides a controlled environment for the growth and propagation of these specific cell lines.
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The RNeasy Mini Kit is a laboratory equipment designed for the purification of total RNA from a variety of sample types, including animal cells, tissues, and other biological materials. The kit utilizes a silica-based membrane technology to selectively bind and isolate RNA molecules, allowing for efficient extraction and recovery of high-quality RNA.
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RPMI 1640 is a common cell culture medium used for the in vitro cultivation of a variety of cells, including human and animal cells. It provides a balanced salt solution and a source of essential nutrients and growth factors to support cell growth and proliferation.
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Penicillin/streptomycin is a commonly used antibiotic solution for cell culture applications. It contains a combination of penicillin and streptomycin, which are broad-spectrum antibiotics that inhibit the growth of both Gram-positive and Gram-negative bacteria.
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The UMUC3 is a laboratory equipment item offered by American Type Culture Collection. It is designed to facilitate the culturing and growth of microbial samples. The core function of the UMUC3 is to provide a controlled environment for the cultivation of various microorganisms.
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Penicillin is a type of antibiotic used in laboratory settings. It is a broad-spectrum antimicrobial agent effective against a variety of bacteria. Penicillin functions by disrupting the bacterial cell wall, leading to cell death.

More about "Urinary Bladder"

The urinary bladder is a crucial organ in the human body, playing a vital role in the urinary system.
It is a hollow, muscular structure that serves as a temporary reservoir for urine before its elimination.
The bladder's walls are composed of smooth muscle tissue, allowing it to expand and contract to accommodate changes in urine volume.
Proper bladder function is essential for maintaining urinary continence and overall urinary tract health.
Researchers studying the urinary bladder often utilize various cell culture techniques and media, such as RPMI 1640 medium, DMEM, and SV-HUC-1 cells.
These tools help them investigate the biology and function of the bladder, as well as potential treatments for related disorders.
The use of reagents like TRIzol and the RNeasy Mini Kit facilitate the extraction and analysis of genetic material from bladder cells, providing insights into gene expression and molecular pathways.
Antibiotic agents like Penicillin and Streptomycin are commonly used in cell culture protocols to prevent microbial contamination, ensuring the integrity of the experimental models.
Additionally, bladder cancer cell lines, such as UMUC3, are frequently employed to study the pathogenesis and potential therapies for this condition.
By leveraging the power of AI-driven platforms like PubCompare.ai, researchers can optimize their urinary bladder research by identifying the most relevant protocols and products from published literature, pre-prints, and patents.
This can enhance the reproducibility and accuracy of their studies, leading to a better understanding of this important organ and the development of more effective treatments for urinary tract disorders.